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Crystal structure of full-length caspase-6 zymogen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 289 0.1M KH2PO4, 0.1M NaH2PO4, 0.1M Bis-tris, 1.75M NaCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.062 α = 90 b = 158.062 β = 90 c = 126.94 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 CCD MARMOSAIC 225 mm CCD 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.697 50 97.6 0.088 6.6 22399 21861 50.69
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3NR2 2.697 33.545 1.33 21743 1116 96.93 0.1825 0.18 0.2313 0.2366 48.8145
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.9376 -2.9376 5.8751
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.441 f_angle_d 1.114 f_chiral_restr 0.076 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3348 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building PHENIX refinement HKL-2000 data reduction SCALA data scaling PHENIX phasing